tbuckley/cabot-search huggingface dataset:
Abstract 4092: Development of nucleotide metabolic reprogrammed CAR T cell therapy suitable for solid tumors
Authors: Yue Hu, Abhijit Sarkar, Kevin Song, Magnus Hook, Andras Heczey, Xiaotong Song
Journal: Cancer Research (2023)

Abstract CAR T cell therapy has represented an exciting breakthrough in the treatment of patients with hematologic malignancies. In contrast, the antitumor activity of CAR T cell therapy in solid tumors has been modest so far in clinical studies. The suboptimal clinical efficacy is a result of multiple factors including limited T cell trafficking, persistence, and the immunosuppressive tumor microenvironment (TME). While current strategies utilize costimulatory molecules and cytokines to activate CAR T cells, a key but largely overlooked problem of CAR T cell therapy is nutrient competition between tumor cells and T cells in the nutrient-poor TME. In our previous studies, a metabolic screen identified inosine as an alternative fuel for T cells which can support T cell growth and function in the absence of glucose. T cells could metabolize inosine into hypoxanthine and phosphorylated ribose by purine nucleoside phosphorylase. Moreover, we demonstrated that T cells have advantage over cancer cells in utilizing inosine, and supplementation with inosine enhances the antitumor efficacy of PD-1 mAb and adoptive T cell transfer in mouse models. In this study, we therefore engineered CAR T cells to express CD26 on the cell surface and a secreted adenosine deaminase (ADA) fused with an anchor. These metabolic reprogrammed CAR (designated as MRCAR) T cells exerts their activities through different mechanisms. ADA irreversibly converts adenosine to inosine, overcoming adenosine-mediated immunosuppression and providing inosine for CAR T cell growth, while CD26 induces a rich chemokine receptor profile enabling CAR T cells to traffic to solid tumors. We demonstrated that CD26-overexpressed CAR T cells displayed superior migration capacity and resisted TGF-beta suppression, while the CD26 expression on unmodified CAR T cells was significantly down-regulated by TGF-beta. We further proved that ADA is conditionally secreted in stress condition (i.e., low pH, lack of nutrient and oxygen) based on ADA’s biological characteristics, suggesting that ADA activates CAR T cells as a trans-signaling to the CAR construct in a tumor specific manner. Remarkably, we observed that the MRCAR T cells inhibit tumor growth more effectively than unmodified CAR T cells in both Huh7 human hepatocellular carcinoma (GPC3-MRCAR) and A549 human non-small cell lung cancer (HER2-MRCAR) mouse models. Thus, MR-CAR T cell therapy represents a promising approach to improve CAR T cell therapy against solid tumors. Citation Format: Yue Hu, Abhijit Sarkar, Kevin Song, Magnus Hook, Andras Heczey, Xiaotong Song. Development of nucleotide metabolic reprogrammed CAR T cell therapy suitable for solid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4092.
Abstract 973: Uncovering gene signatures of Ewings sarcoma drug sensitivity during the evolution of resistance
Authors: Kristi Lin-Rahardja, Jessica Scarborough, Masahiro Hitomi, Jacob G. Scott
Journal: Cancer Research (2023)

Abstract The evolution of chemotherapeutic resistance can cause treatment failure in patients with metastatic Ewings sarcoma (EWS), a rare pediatric bone cancer. As resistance to the first-line therapy evolves, there is potential for the tumor to develop sensitivities to other chemotherapeutic agents besides the active treatment. This concept is known as collateral sensitivity, and it presents an opportunity for medical providers to plan more effective treatment regimens. However, it can be difficult to predict due to the stochastic nature of evolution. By analyzing gene expression patterns among independent populations of an EWS cell line that have repeatedly evolved collateral responses, we aim to extract a collection of gene signatures, or sets of genes, that will predict states of collateral sensitivity against various existing chemotherapies. To accomplish this, we will treat independently evolving replicates of an EWS cell line (A673) with the standard-of-care therapy to evolve resistance. Throughout this treatment regimen, we will regularly screen for collateral sensitivity against 100 FDA-approved cancer drugs and perform bulk RNA-sequencing. When collateral sensitivity against a drug is observed, we will utilize the RNA-sequencing data to extract gene signatures using differential expression analysis. The signatures will then be validated using patient-derived xenografts collected in our lab as well as from collaborators. When completed, the sizable archive of sensitivity signatures we expect to assemble could greatly streamline the process of treatment planning for EWS patients, especially those with advanced disease. When a patient's response to primary therapy begins to decline, RNA- sequencing can be performed on a tumor biopsy, gene expression patterns can be compared with the validated signature library, and the most appropriate drug for the individual patient can be determined and used for subsequent treatment. Using this method, a patient's sensitivity profile can be reassessed at any point. This proposed method of treatment planning mitigates the need for excessive treatment regimens that are not guaranteed to be effective for every patient, thereby expanding the reach of precision medicine and potentially improving outcomes for EWS patients. Citation Format: Kristi Lin-Rahardja, Jessica Scarborough, Masahiro Hitomi, Jacob G. Scott. Uncovering gene signatures of Ewings sarcoma drug sensitivity during the evolution of resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 973.
Abstract 5940: Enhanced mast cell abundance is associated with the enrichment of CCR2+ cytotoxic T cells and favorable prognosis in lung adenocarcinoma
Authors: Fan Fan, Xiaoming Zhang, Haiquan Chen
Journal: Cancer Research (2023)

Abstract Mast cells constitute indispensably immunoregulatory sentinel cells in tumor microenvironment, however, their functions are poorly characterized in lung adenocarcinoma (LUAD). Here, we performed flow cytometry and single-cell RNA sequencing to comprehensively characterize LUAD infiltrating MCs. MCs exhibited remarkably functional heterogeneity and were enriched in ground-glass opacity featured LUAD (gLUAD). The MCs in gLUAD exhibited proinflammatory and chemotactic properties while the MCs in radiologically solid LUAD (sLUAD) were associated with tumor angiogenesis. MCs were an important source of CCL2 that correlated with the recruitment of CCR2+ cytotoxic T lymphocytes (CTLs), which represent a specific subcluster of pre-exhausted T cells with tissue-resident memory phenotype and enhanced cytotoxicity. Increased infiltration of MCs-CCR2+ CTLs and their colocalization showed a strong association with favorable prognosis after surgery but were not associated with improved survival after chemotherapy. Collectively, these findings reveal a key role of MCs in LUAD and their potential crosstalk with CTLs, suggesting that targeting MCs may be a novel immunotherapeutic strategy for LUAD. Citation Format: Fan Fan, Xiaoming Zhang, Haiquan Chen. Enhanced mast cell abundance is associated with the enrichment of CCR2+ cytotoxic T cells and favorable prognosis in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5940.
Abstract 1490: Exon exclusion of NELF-E produces an anti-tumorigenic truncated isoform in hepatocellular carcinoma
Authors: Laura Reynolds, Ryan Lamm, Anna Barry, Meghan Grim, Kai Zhang, Hien Dang
Journal: Cancer Research (2023)

Abstract Overexpression of negative elongation factor E (NELF-E), a subunit of the negative elongation factor (NELF) complex involved in transcription pausing, has been implicated in poor hepatocellular carcinoma (HCC) outcome. We recently discovered an intronic heterozygous single nucleotide polymorphism (SNP), rs79208225 (G&amp;gt;A), near a spliceosome binding site in less than 1% of the general population but ~4% of our HCC cohort. HCC patients with the SNP had significantly longer times till recurrence (p=0.001) and better overall survival (p=0.02) compared to patients without the SNP. Using the minigene assay, we found the SNP causes exon 10 exclusion, which resulted in lower levels of full length NELF-E and the presence of a truncated NELF-E isoform that was not degraded via RNAi surveillance. We hypothesize NELF-E isoform switching is anti-tumorigenic in HCC. To investigate the effects of exon 10 exclusion, we employed antisense oligonucleotides (ASOs). HCC cells treated with ASOs had decreased cell proliferation and colony formation. Moreover, exon 10 exclusion enriched for the truncated NELF-E isoform and decreased full length mRNA and protein expression. Genetic models (CRISPR/cas9) showed similar phenotypes, suggesting that the truncated NELF-E is anti-tumorigenic. Currently, we are investigating the functional role of the truncated NELF-E protein in transcription regulation and the effects of isoform switching in HCC cells as a potential therapeutic strategy for HCCs with elevated NELF-E levels. Citation Format: Laura Reynolds, Ryan Lamm, Anna Barry, Meghan Grim, Kai Zhang, Hien Dang. Exon exclusion of NELF-E produces an anti-tumorigenic truncated isoform in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1490.
Abstract 2771: KSQ-4279 mediated USP1 inhibition induces replication associated DNA gaps that contribute to cell death
Authors: Sumeet Nayak, Pamela Sullivan, Yuji Mishina, Anne Dodson, Pei-Lun Kao, Hugh Gannon, Chris Middleton, Sol Shenker, Morgan Murray, Michael Schlabach, Frank Stegmeier, Erica Tobin, Louise Cadzow, Andrew Wylie
Journal: Cancer Research (2023)

Abstract Tumors with defects in DNA double strand break (DSB) repair pathways, including those with mutations in BRCA1/2, are often treated with either poly (ADP-ribose) polymerase-1 (PARP1) inhibitors or platinum-based chemotherapy. Despite their clinical benefits, many patients develop resistance leading to the need for novel therapeutic approaches. To address this unmet clinical need, we applied our CRISPRomics® platform to identify novel therapeutic targets for DNA damage and repair deficient cancers. One of the top ranked targets was the deubiquitinating enzyme, USP1, with known functions in DNA damage repair pathways of translesion synthesis (TLS) and fanconi anemia (FA). We developed a novel small molecule inhibitor, KSQ-4279, that selectively inhibits USP1 and leads to accumulation of mono-ubiquitinated USP1 substrates such as proliferating nuclear antigen (PCNA). In addition to KSQ-4279’s activity in BRCA mutant tumors with known homologous recombination deficiencies (HRD), KSQ-4279 also exhibits synergistic activity in combination with PARP inhibitors and re-sensitizes PARP refractory tumors. Mechanistically, we show that in sensitive cell lines, treatment with KSQ-4279 alters the replication fork dynamics resulting in replication stress via induction of replication associated single stranded DNA gaps and subsequent fork degradation. Additionally, KSQ-4279 leads to loss of the essential DNA replication and repair protein, PCNA, which can be rescued by blocking PCNA ubiquitination either through Rad18 knockout or by ectopic expression of a PCNA K164R mutant. This loss of PCNA and sensitizing ssDNA lesions eventually lead to DNA double strand breaks (DSBs) and wide-spread DNA damage accumulation that contributes to cell death. This mechanistic insight supports the ongoing clinical trial of KSQ-4279 in patients with tumors harboring BRCA1/2 or other HRD mutations, both as a single agent and in combination with PARP inhibitors. Citation Format: Sumeet Nayak, Pamela Sullivan, Yuji Mishina, Anne Dodson, Pei-Lun Kao, Hugh Gannon, Chris Middleton, Sol Shenker, Morgan Murray, Michael Schlabach, Frank Stegmeier, Erica Tobin, Louise Cadzow, Andrew Wylie. KSQ-4279 mediated USP1 inhibition induces replication associated DNA gaps that contribute to cell death [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2771.
Abstract 3202: NanoBiT technologies for CAR-T characterization and potency testing
Authors: Julia K. Gilden, Pete Stecha, Aileen Paguio, Jim Hartnett, Brock Binkowski, Dan Lazar, Frank Fan, Mei Cong
Journal: Cancer Research (2023)

Abstract Despite significant clinical advances in CAR-T cell therapies for cancer, the ability to precisely and reproducibly analyze the potency of these drug products remains a challenge. As new CAR-T products and production methodologies are developed, it is becoming increasingly important to be able to rigorously evaluate the relative potencies of each batch. We have developed two MOA-based bioluminescent assays that overcome challenges in quantitative assessment of T cell therapies. Both assays rely on split NanoBiT luciferase technology. In the HiBiT Target Cell Killing Assay, incubation of CAR-T cells with target cells stably expressing HiBiT results in lysis of the target cells and release of HiBiT proteins. These HiBiT proteins bind with high affinity to LgBiT in the detection reagent and form functional NanoBiT luciferase, resulting in production of light in proportion to target cell lysis. Lumit Immunoassays are a simple and homogeneous method for measuring cytokine production from engineered T cells. Monoclonal antibodies are covalently labeled with LgBiT and a low-affinity tag, SmBiT, which have negligible association in solution. When the antibodies are brought together by a common analyte, such as a cytokine, SmBiT and LgBiT can compliment to form NanoBiT luciferase and produce light in proportion to the concentration of analyte in the sample. Lumit Immunoassays can be run directly on cells, removing media transfer, dilution, and wash steps that can be common sources of error. These luminescent assays are homogenous, fast, highly sensitive, and have robust assay windows. They represent a new set of tools for development and characterization of T cell-based immunotherapies. Citation Format: Julia K. Gilden, Pete Stecha, Aileen Paguio, Jim Hartnett, Brock Binkowski, Dan Lazar, Frank Fan, Mei Cong. NanoBiT technologies for CAR-T characterization and potency testing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3202.
Abstract 4274: Functional dissection of complex tissue microenvironment using spatial transcriptomics data
Authors: Xinyu Zhou, Alexander White, Tingbo Guo, Pengtao Dang, Yuhui Wei, Xiao Wang, Kaman So, Chi Zhang, Sha Cao
Journal: Cancer Research (2023)

Abstract Spatial transcriptomics (ST) data holds enormous potential to provide new perspectives for biologists seeking to understand the tumor tissue microenvironments. Cells in the same microenvironment are always exposed to biochemical conditions displacing specific spatial patterns. To truly dismantle the tissue microenvironment heterogeneity as well as cells’ diverse responses to the variable microenvironment, we rely on spatial information to dissect the tissue into different functional regions, which are spatially dependent and biologically meaningful. We have developed a statistical method, smooth Low Rank approximation and Clustering (smoothLRC) to model the spatial transcriptomic data as its low-rank approximation with spatial smoothness. smoothLRC accomplishes this by extracting the latent low-rank structure of the expression profiles. We present a regularized maximum likelihood estimator approximating the noisy observed expression matrix. This estimator incorporates spatial information and addresses expression dropout. It uses a low-rank Poisson distribution to account for the noise that plagues ST-based gene expression data with severe dropout events and a spatial smoothness penalty to encourage neighboring cells to fall into the same functional region. A dropout is an event where genes expressed in a given cell or region are incorrectly measured as unexpressed. SmoothLRC has the following key features: 1) it is a statistically rigorous method; 2) the spatially smooth low-rank subspace could enable meaningful functional dissection, which is an unprecedented capability; 3) the low-rank structures could be used to recover the original expression, saving many expression values that are not captured. Citation Format: Xinyu Zhou, Alexander White, Tingbo Guo, Pengtao Dang, Yuhui Wei, Xiao Wang, Kaman So, Chi Zhang, Sha Cao. Functional dissection of complex tissue microenvironment using spatial transcriptomics data. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4274.
Abstract 5183: Development of an aerosol-based immunotherapy for lung cancer
Authors: Yongren Li, Zhen Zhao, John Fetse, Reaid Hasan, Umar-Farouk Mamani, Yuhan Guo, Kun Cheng
Journal: Cancer Research (2023)

Abstract Lung cancer is one of the leading causes of cancer death and the second most cancer in the world. Compared to systematic administration, local delivery of therapeutic agents to the lung increases their accumulation in lung cancer cells and reduces the toxicity in other organs. We previously discovered an anti-PD-L1 peptide that can be potentially uses for lung cancer therapy. This project aims to develop an aerosolized formulation of the anti-PD-L1 peptide for the treatment of lung cancer. We hypothesize that the aerosolized peptide has higher accumulation in the lung compared to systematic formulations, leading to high therapeutic index with less side effects. We developed a spray freeze-drying procedure and optimized the formulation to prepare the peptide dry powders. The median mass aerodynamic diameter (MMAD) and geometric standard deviation (GSD) of the aerosols were determined by an 8-stage Andersen Cascade Impactor. The morphology of the aerosols was studied using a scanning electron microscope (SEM). The stability of the aerosols in lung fluid was evaluated. Blocking assay suggested that the aerosolized formulation maintains the blocking efficiency of the peptide. Intratracheal administration of the peptide dry powder shows a high accumulation of the peptide in the lung. Citation Format: Yongren Li, Zhen Zhao, John Fetse, Reaid Hasan, Umar-Farouk Mamani, Yuhan Guo, Kun Cheng. Development of an aerosol-based immunotherapy for lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5183.
Abstract 1619: Generation of a novel estrogen receptor degrader
Authors: Yuan Liu, Jason R. Kennerdell, Bo Lin, Mads B. Larsen, Irene Alfaras, Daniel P. Camarco, Ferhan Tuncer, Toren Finkel, Bill B. Chen
Journal: Cancer Research (2023)

Abstract Fulvestrant is an effective therapy to treat post-menopausal women with estrogen receptor (ER)-positive metastatic breast cancer. The compound works as a selective estrogen receptor degrader (SERD). Structurally similar to estrogen, fulvestrant binds to the ligand binding domain (LBD) of the ER, altering the stability of the protein, leading to its accelerated proteasomal degradation. While effective, fulvestrant must be given intramuscularly, which has limited its clinical adoption. Based on the success of fulvestrant, multiple attempts have been made to generate orally available SERDs. These attempts have focused on compounds that, like fulvestrant, bind within the LBD of the ER. Overall, these intensive efforts have generated limited success. We reasoned that it may be possible to identify potential SERDs that bind to the ER in regions outside the LBD. Such an approach would be useful for tumors bearing wildtype ER, and likely for those bearing a mutant form of the ER, since most mutations cluster in the LBD. We have recently developed a high throughput platform that allows for the identification of ligands that can bind to wide variety of protein targets. Using this approach, we screened a diverse chemical library of 100,000 small molecules to identify compounds that bind outside of the LBD, and in particular to the N-terminal region of the ER. This strategy identified CL-ER-100, a small molecule that directly bound to the N-terminal region of the ER and functioned as a SERD. While CL-ER-100 rapidly induced ER proteasomal-dependent degradation, it had no effect on the protein levels of other, structurally related nuclear receptors. Based on its structure and size (~ MW 300 Da), CL-ER-100 is expected to have excellent bioavailability. Consistent with its binding outside of the LBD, addition of tamoxifen had no effect on the ability of CL-ER-100 to induce ER protein degradation. In cells, CL-ER-100 was able to markedly inhibit the growth of breast cancer cell lines such as MCF7 and T47D (IC50 of ~ 100 nM) while not inhibiting the growth of a wide array of normal and non-breast cancer tumor cell lines. Taken together, these results identify a novel strategy to develop small molecule SERDs that induce ER protein degradation by binding to previously untargeted regions of the estrogen receptor. Citation Format: Yuan Liu, Jason R. Kennerdell, Bo Lin, Mads B. Larsen, Irene Alfaras, Daniel P. Camarco, Ferhan Tuncer, Toren Finkel, Bill B. Chen. Generation of a novel estrogen receptor degrader [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1619.